fix: preserve LAMMPS configuration indices

[njzjz-bot]

Summary

• copy caller configuration before normalization
• preserve an explicit conf_idx value
• add the empty workaround only when the key is absent
• cover the exported helper with an explicit index regression test

Tests

• PYTHONPATH=tests python -m unittest -v tests.exploration.test_make_task_group_from_config.TestMakeLmpTaskGroupFromConfig.test_npt_preserves_explicit_conf_idx tests.exploration.test_make_task_group_from_config.TestMakeLmpTaskGroupFromConfig.test_npt
• ruff format --check dpgen2/exploration/task/make_task_group_from_config.py tests/exploration/test_make_task_group_from_config.py
• isort --check-only dpgen2/exploration/task/make_task_group_from_config.py tests/exploration/test_make_task_group_from_config.py
• git diff --check

Closes #358

Coding agent: Codex
Codex version: codex-cli 0.149.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

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Run ID: 70719375-686e-4019-8c92-01b42e2b86c4

📥 Commits

Reviewing files that changed from the base of the PR and between 6b01f29 and 83808a2.

📒 Files selected for processing (2)

• dpgen2/exploration/task/make_task_group_from_config.py
• tests/exploration/test_make_task_group_from_config.py

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.43%. Comparing base (6b01f29) to head (83808a2).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #384   +/-   ##
=======================================
  Coverage   84.43%   84.43%           
=======================================
  Files         104      104           
  Lines        6110     6111    +1     
=======================================
+ Hits         5159     5160    +1     
  Misses        951      951           

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Retracted. This review was produced without running the mandated /code-review fan-out (the loop skill's section 2); the substitute process used instead has since been shown to miss findings and, in one case, to state a verified-sounding falsehood. Re-reviewing properly.